Tried all three, it's most noticeable with the headphones (KRK over-ear.) I can minimize the effect by dimeing the channel volume and master and turning the gain nearly off but it's still there, it sounds for all the world as though I have one amp set to clean and another, much quieter, with fuzz on it playing in the background.
I left the entire first bank untouched so all the original sounds are there, it's really not subtle. No clean sounds are really clean, except the "no amp" option which doesn't seem to be affected. Also I'm not cranking the outboards volume knob, definitely not overdriving the headphones themselves.